Starting phenix.real_space_refine on Sat Aug 8 14:17:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10rx_75424/08_2026/10rx_75424_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/10rx_75424/08_2026/10rx_75424.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/10rx_75424/08_2026/10rx_75424_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10rx_75424/08_2026/10rx_75424_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/10rx_75424/08_2026/10rx_75424.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10rx_75424/08_2026/10rx_75424.map" } resolution = 2.51 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 16 5.49 5 S 28 5.16 5 C 8876 2.51 5 N 2104 2.21 5 O 2324 1.98 5 H 13116 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26464 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 6421 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 24, 'TRANS': 370} Chain breaks: 1 Chain: "B" Number of atoms: 6421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 6421 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 24, 'TRANS': 370} Chain breaks: 1 Chain: "C" Number of atoms: 6421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 6421 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 24, 'TRANS': 370} Chain breaks: 1 Chain: "D" Number of atoms: 6421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 6421 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 24, 'TRANS': 370} Chain breaks: 1 Chain: "A" Number of atoms: 235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 235 Unusual residues: {'PCW': 9} Classifications: {'RNAv2': 1, 'undetermined': 9} Modifications used: {'rna3p': 1} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 273 Unresolved non-hydrogen angles: 326 Unresolved non-hydrogen dihedrals: 253 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PCW:plan-2': 6, 'PCW:plan-4': 4, 'PCW:plan-1': 4, 'PCW:plan-3': 5} Unresolved non-hydrogen planarities: 69 Chain: "B" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 195 Unusual residues: {'PCW': 8} Classifications: {'RNAv2': 1, 'undetermined': 8} Modifications used: {'rna3p': 1} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 259 Unresolved non-hydrogen angles: 312 Unresolved non-hydrogen dihedrals: 239 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PCW:plan-4': 4, 'PCW:plan-1': 4, 'PCW:plan-2': 5, 'PCW:plan-3': 5} Unresolved non-hydrogen planarities: 65 Chain: "C" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 195 Unusual residues: {'PCW': 8} Classifications: {'RNAv2': 1, 'undetermined': 8} Modifications used: {'rna3p': 1} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 259 Unresolved non-hydrogen angles: 312 Unresolved non-hydrogen dihedrals: 239 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PCW:plan-4': 4, 'PCW:plan-1': 4, 'PCW:plan-2': 5, 'PCW:plan-3': 5} Unresolved non-hydrogen planarities: 65 Chain: "D" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 155 Unusual residues: {'PCW': 7} Classifications: {'RNAv2': 1, 'undetermined': 7} Modifications used: {'rna3p': 1} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 245 Unresolved non-hydrogen angles: 298 Unresolved non-hydrogen dihedrals: 225 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PCW:plan-4': 4, 'PCW:plan-1': 4, 'PCW:plan-2': 4, 'PCW:plan-3': 5} Unresolved non-hydrogen planarities: 61 Time building chain proxies: 5.14, per 1000 atoms: 0.19 Number of scatterers: 26464 At special positions: 0 Unit cell: (105.3, 105.3, 119.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 28 16.00 P 16 15.00 O 2324 8.00 N 2104 7.00 C 8876 6.00 H 13116 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.90 Conformation dependent library (CDL) restraints added in 993.2 milliseconds 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3000 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 8 sheets defined 72.2% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 9 through 36 removed outlier: 3.788A pdb=" N LEU A 13 " --> pdb=" O PRO A 9 " (cutoff:3.500A) Proline residue: A 31 - end of helix Processing helix chain 'A' and resid 37 through 40 Processing helix chain 'A' and resid 43 through 64 removed outlier: 4.000A pdb=" N ILE A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) Proline residue: A 59 - end of helix Processing helix chain 'A' and resid 80 through 87 removed outlier: 4.492A pdb=" N ASP A 84 " --> pdb=" O SER A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 99 Processing helix chain 'A' and resid 101 through 106 Processing helix chain 'A' and resid 107 through 112 Processing helix chain 'A' and resid 113 through 126 removed outlier: 4.267A pdb=" N SER A 117 " --> pdb=" O LEU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 159 Processing helix chain 'A' and resid 165 through 182 Processing helix chain 'A' and resid 193 through 224 Processing helix chain 'A' and resid 227 through 246 Processing helix chain 'A' and resid 249 through 268 Processing helix chain 'A' and resid 271 through 277 Processing helix chain 'A' and resid 280 through 293 Processing helix chain 'A' and resid 294 through 299 Processing helix chain 'A' and resid 300 through 303 removed outlier: 3.591A pdb=" N LYS A 303 " --> pdb=" O PRO A 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 300 through 303' Processing helix chain 'A' and resid 306 through 315 Processing helix chain 'A' and resid 367 through 372 removed outlier: 3.517A pdb=" N LEU A 371 " --> pdb=" O GLU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 403 removed outlier: 3.856A pdb=" N ARG A 403 " --> pdb=" O ARG A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 414 Processing helix chain 'B' and resid 10 through 36 Proline residue: B 31 - end of helix Processing helix chain 'B' and resid 37 through 40 Processing helix chain 'B' and resid 43 through 64 removed outlier: 4.000A pdb=" N ILE B 58 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Proline residue: B 59 - end of helix Processing helix chain 'B' and resid 80 through 87 removed outlier: 4.492A pdb=" N ASP B 84 " --> pdb=" O SER B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 99 Processing helix chain 'B' and resid 101 through 106 Processing helix chain 'B' and resid 107 through 112 Processing helix chain 'B' and resid 113 through 126 removed outlier: 4.267A pdb=" N SER B 117 " --> pdb=" O LEU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 159 Processing helix chain 'B' and resid 165 through 182 Processing helix chain 'B' and resid 193 through 224 Processing helix chain 'B' and resid 227 through 246 Processing helix chain 'B' and resid 249 through 268 Processing helix chain 'B' and resid 271 through 277 Processing helix chain 'B' and resid 280 through 293 Processing helix chain 'B' and resid 294 through 299 Processing helix chain 'B' and resid 300 through 303 removed outlier: 3.591A pdb=" N LYS B 303 " --> pdb=" O PRO B 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 300 through 303' Processing helix chain 'B' and resid 306 through 315 Processing helix chain 'B' and resid 367 through 372 removed outlier: 3.516A pdb=" N LEU B 371 " --> pdb=" O GLU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 403 removed outlier: 3.856A pdb=" N ARG B 403 " --> pdb=" O ARG B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 414 Processing helix chain 'C' and resid 10 through 36 Proline residue: C 31 - end of helix Processing helix chain 'C' and resid 37 through 40 Processing helix chain 'C' and resid 43 through 64 removed outlier: 4.000A pdb=" N ILE C 58 " --> pdb=" O LEU C 54 " (cutoff:3.500A) Proline residue: C 59 - end of helix Processing helix chain 'C' and resid 80 through 87 removed outlier: 4.491A pdb=" N ASP C 84 " --> pdb=" O SER C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 99 Processing helix chain 'C' and resid 101 through 106 Processing helix chain 'C' and resid 107 through 112 Processing helix chain 'C' and resid 113 through 126 removed outlier: 4.267A pdb=" N SER C 117 " --> pdb=" O LEU C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 159 Processing helix chain 'C' and resid 165 through 182 Processing helix chain 'C' and resid 193 through 224 Processing helix chain 'C' and resid 227 through 246 Processing helix chain 'C' and resid 249 through 268 Processing helix chain 'C' and resid 271 through 277 Processing helix chain 'C' and resid 280 through 293 Processing helix chain 'C' and resid 294 through 299 Processing helix chain 'C' and resid 300 through 303 removed outlier: 3.591A pdb=" N LYS C 303 " --> pdb=" O PRO C 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 300 through 303' Processing helix chain 'C' and resid 306 through 315 Processing helix chain 'C' and resid 367 through 372 removed outlier: 3.517A pdb=" N LEU C 371 " --> pdb=" O GLU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 403 removed outlier: 3.856A pdb=" N ARG C 403 " --> pdb=" O ARG C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 414 Processing helix chain 'D' and resid 10 through 36 Proline residue: D 31 - end of helix Processing helix chain 'D' and resid 37 through 40 Processing helix chain 'D' and resid 43 through 64 removed outlier: 4.000A pdb=" N ILE D 58 " --> pdb=" O LEU D 54 " (cutoff:3.500A) Proline residue: D 59 - end of helix Processing helix chain 'D' and resid 80 through 87 removed outlier: 4.492A pdb=" N ASP D 84 " --> pdb=" O SER D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 99 Processing helix chain 'D' and resid 101 through 106 Processing helix chain 'D' and resid 107 through 112 Processing helix chain 'D' and resid 113 through 126 removed outlier: 4.267A pdb=" N SER D 117 " --> pdb=" O LEU D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 159 Processing helix chain 'D' and resid 165 through 182 Processing helix chain 'D' and resid 193 through 224 Processing helix chain 'D' and resid 227 through 246 Processing helix chain 'D' and resid 249 through 268 Processing helix chain 'D' and resid 271 through 277 Processing helix chain 'D' and resid 280 through 293 Processing helix chain 'D' and resid 294 through 299 Processing helix chain 'D' and resid 300 through 303 removed outlier: 3.591A pdb=" N LYS D 303 " --> pdb=" O PRO D 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 300 through 303' Processing helix chain 'D' and resid 306 through 315 Processing helix chain 'D' and resid 367 through 372 removed outlier: 3.517A pdb=" N LEU D 371 " --> pdb=" O GLU D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 403 removed outlier: 3.856A pdb=" N ARG D 403 " --> pdb=" O ARG D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 414 Processing sheet with id=AA1, first strand: chain 'A' and resid 318 through 322 Processing sheet with id=AA2, first strand: chain 'A' and resid 327 through 329 removed outlier: 6.441A pdb=" N TYR A 327 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ALA A 383 " --> pdb=" O TYR A 327 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 318 through 322 Processing sheet with id=AA4, first strand: chain 'B' and resid 327 through 329 removed outlier: 6.440A pdb=" N TYR B 327 " --> pdb=" O ALA B 383 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ALA B 383 " --> pdb=" O TYR B 327 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 318 through 322 Processing sheet with id=AA6, first strand: chain 'C' and resid 327 through 329 removed outlier: 6.441A pdb=" N TYR C 327 " --> pdb=" O ALA C 383 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ALA C 383 " --> pdb=" O TYR C 327 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 318 through 322 Processing sheet with id=AA8, first strand: chain 'D' and resid 327 through 329 removed outlier: 6.440A pdb=" N TYR D 327 " --> pdb=" O ALA D 383 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ALA D 383 " --> pdb=" O TYR D 327 " (cutoff:3.500A) 852 hydrogen bonds defined for protein. 2436 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.36 Time building geometry restraints manager: 2.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 13108 1.03 - 1.23: 47 1.23 - 1.42: 5345 1.42 - 1.62: 8160 1.62 - 1.81: 76 Bond restraints: 26736 Sorted by residual: bond pdb=" C4 CMP C 501 " pdb=" C5 CMP C 501 " ideal model delta sigma weight residual 1.490 1.333 0.157 2.00e-02 2.50e+03 6.12e+01 bond pdb=" C4 CMP D 501 " pdb=" C5 CMP D 501 " ideal model delta sigma weight residual 1.490 1.334 0.156 2.00e-02 2.50e+03 6.11e+01 bond pdb=" C4 CMP A 501 " pdb=" C5 CMP A 501 " ideal model delta sigma weight residual 1.490 1.334 0.156 2.00e-02 2.50e+03 6.11e+01 bond pdb=" C4 CMP B 501 " pdb=" C5 CMP B 501 " ideal model delta sigma weight residual 1.490 1.334 0.156 2.00e-02 2.50e+03 6.10e+01 bond pdb=" O2P CMP D 501 " pdb=" P CMP D 501 " ideal model delta sigma weight residual 1.510 1.643 -0.133 2.00e-02 2.50e+03 4.44e+01 ... (remaining 26731 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.25: 47939 5.25 - 10.51: 137 10.51 - 15.76: 40 15.76 - 21.01: 0 21.01 - 26.27: 8 Bond angle restraints: 48124 Sorted by residual: angle pdb=" C19 PCW A 504 " pdb=" C20 PCW A 504 " pdb=" C21 PCW A 504 " ideal model delta sigma weight residual 127.82 154.09 -26.27 3.00e+00 1.11e-01 7.67e+01 angle pdb=" C19 PCW C 503 " pdb=" C20 PCW C 503 " pdb=" C21 PCW C 503 " ideal model delta sigma weight residual 127.82 154.07 -26.25 3.00e+00 1.11e-01 7.66e+01 angle pdb=" C19 PCW D 503 " pdb=" C20 PCW D 503 " pdb=" C21 PCW D 503 " ideal model delta sigma weight residual 127.82 154.07 -26.25 3.00e+00 1.11e-01 7.65e+01 angle pdb=" C19 PCW B 502 " pdb=" C20 PCW B 502 " pdb=" C21 PCW B 502 " ideal model delta sigma weight residual 127.82 154.05 -26.23 3.00e+00 1.11e-01 7.64e+01 angle pdb=" C19 PCW D 502 " pdb=" C20 PCW D 502 " pdb=" C21 PCW D 502 " ideal model delta sigma weight residual 127.82 154.04 -26.22 3.00e+00 1.11e-01 7.64e+01 ... (remaining 48119 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.34: 12112 32.34 - 64.69: 540 64.69 - 97.03: 28 97.03 - 129.38: 8 129.38 - 161.72: 12 Dihedral angle restraints: 12700 sinusoidal: 7252 harmonic: 5448 Sorted by residual: dihedral pdb=" N PCW C 509 " pdb=" C4 PCW C 509 " pdb=" C5 PCW C 509 " pdb=" O4P PCW C 509 " ideal model delta sinusoidal sigma weight residual -66.66 95.06 -161.72 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" N PCW A 502 " pdb=" C4 PCW A 502 " pdb=" C5 PCW A 502 " pdb=" O4P PCW A 502 " ideal model delta sinusoidal sigma weight residual -66.66 95.05 -161.71 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" N PCW B 509 " pdb=" C4 PCW B 509 " pdb=" C5 PCW B 509 " pdb=" O4P PCW B 509 " ideal model delta sinusoidal sigma weight residual -66.66 95.05 -161.71 1 3.00e+01 1.11e-03 2.08e+01 ... (remaining 12697 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1716 0.048 - 0.096: 341 0.096 - 0.144: 51 0.144 - 0.192: 1 0.192 - 0.240: 11 Chirality restraints: 2120 Sorted by residual: chirality pdb=" C2' CMP A 501 " pdb=" C1' CMP A 501 " pdb=" C3' CMP A 501 " pdb=" O2' CMP A 501 " both_signs ideal model delta sigma weight residual False -2.51 -2.75 0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" C2' CMP D 501 " pdb=" C1' CMP D 501 " pdb=" C3' CMP D 501 " pdb=" O2' CMP D 501 " both_signs ideal model delta sigma weight residual False -2.51 -2.75 0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" C2' CMP B 501 " pdb=" C1' CMP B 501 " pdb=" C3' CMP B 501 " pdb=" O2' CMP B 501 " both_signs ideal model delta sigma weight residual False -2.51 -2.75 0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 2117 not shown) Planarity restraints: 3704 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 89 " -0.029 5.00e-02 4.00e+02 4.38e-02 3.07e+00 pdb=" N PRO D 90 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO D 90 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 90 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 89 " -0.029 5.00e-02 4.00e+02 4.35e-02 3.03e+00 pdb=" N PRO C 90 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO C 90 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 90 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 89 " 0.029 5.00e-02 4.00e+02 4.35e-02 3.03e+00 pdb=" N PRO A 90 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 90 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 90 " 0.024 5.00e-02 4.00e+02 ... (remaining 3701 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.36: 9463 2.36 - 2.92: 62149 2.92 - 3.48: 73810 3.48 - 4.04: 97714 4.04 - 4.60: 147877 Nonbonded interactions: 391013 Sorted by model distance: nonbonded pdb=" OD1 ASP C 92 " pdb=" H LEU C 93 " model vdw 1.799 2.450 nonbonded pdb=" OD1 ASP B 92 " pdb=" H LEU B 93 " model vdw 1.799 2.450 nonbonded pdb=" OD1 ASP D 92 " pdb=" H LEU D 93 " model vdw 1.799 2.450 nonbonded pdb=" OD1 ASP A 92 " pdb=" H LEU A 93 " model vdw 1.799 2.450 nonbonded pdb=" HH TYR D 25 " pdb=" OD1 ASP D 47 " model vdw 1.830 2.450 ... (remaining 391008 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 9 through 501 or (resid 502 and (name C1 or name C11 or na \ me C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name O11 o \ r name O2 or name O3 or name O31 or name O3P or name P )) or (resid 503 and (nam \ e C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or \ name C17 or name C18 or name C19 or name C2 or name C20 or name C21 or name C22 \ or name C23 or name C3 or name C31 or name C32 or name C33 or name C34 or name C \ 35 or name C36 or name O11 or name O2 or name O3 or name O31 or name O3P or name \ P )) or (resid 504 and (name C33 or name C34 or name C35 or name C36 or name C3 \ 7 or name C38 or name C39 or name C40)) or resid 505 or (resid 506 and (name C36 \ or name C37 or name C38 or name C39 or name C40 or name C41 or name C42 or name \ C43 or name C44 or name C45)))) selection = (chain 'B' and (resid 9 through 501 or (resid 502 and (name C1 or name C11 or na \ me C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name O11 o \ r name O2 or name O3 or name O31 or name O3P or name P )) or (resid 503 and (nam \ e C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or \ name C17 or name C18 or name C19 or name C2 or name C20 or name C21 or name C22 \ or name C23 or name C3 or name C31 or name C32 or name C33 or name C34 or name C \ 35 or name C36 or name O11 or name O2 or name O3 or name O31 or name O3P or name \ P )) or (resid 504 and (name C33 or name C34 or name C35 or name C36 or name C3 \ 7 or name C38 or name C39 or name C40)) or resid 505 through 506)) selection = (chain 'C' and (resid 9 through 501 or (resid 502 and (name C1 or name C11 or na \ me C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name O11 o \ r name O2 or name O3 or name O31 or name O3P or name P )) or (resid 503 and (nam \ e C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or \ name C17 or name C18 or name C19 or name C2 or name C20 or name C21 or name C22 \ or name C23 or name C3 or name C31 or name C32 or name C33 or name C34 or name C \ 35 or name C36 or name O11 or name O2 or name O3 or name O31 or name O3P or name \ P )) or (resid 504 and (name C33 or name C34 or name C35 or name C36 or name C3 \ 7 or name C38 or name C39 or name C40)) or resid 505 through 506)) selection = (chain 'D' and (resid 9 through 501 or (resid 502 and (name C1 or name C11 or na \ me C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name O11 o \ r name O2 or name O3 or name O31 or name O3P or name P )) or (resid 503 and (nam \ e C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or \ name C17 or name C18 or name C19 or name C2 or name C20 or name C21 or name C22 \ or name C23 or name C3 or name C31 or name C32 or name C33 or name C34 or name C \ 35 or name C36 or name O11 or name O2 or name O3 or name O31 or name O3P or name \ P )) or (resid 504 and (name C33 or name C34 or name C35 or name C36 or name C3 \ 7 or name C38 or name C39 or name C40)) or resid 505 through 506)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.160 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 27.100 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.157 13620 Z= 0.529 Angle : 1.289 26.267 18388 Z= 0.489 Chirality : 0.041 0.240 2120 Planarity : 0.004 0.044 2228 Dihedral : 19.275 161.723 5316 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 0.22 % Allowed : 14.31 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.60 (0.22), residues: 1564 helix: 2.51 (0.16), residues: 1048 sheet: -2.77 (0.54), residues: 68 loop : 0.67 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 399 TYR 0.009 0.001 TYR C 245 PHE 0.008 0.001 PHE C 365 TRP 0.007 0.001 TRP D 264 HIS 0.002 0.001 HIS D 281 Details of bonding type rmsd/Z covalent geometry : bond 0.01060 / 0.53 (13620) covalent geometry : angle 1.28911 / 0.49 (18388) hydrogen bonds : bond 0.08964 / 6.57 ( 852) hydrogen bonds : angle 4.70111 / 3.45 ( 2436) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ILE cc_start: 0.8862 (tt) cc_final: 0.8612 (pp) outliers start: 3 outliers final: 3 residues processed: 66 average time/residue: 0.7329 time to fit residues: 55.6181 Evaluate side-chains 54 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain D residue 47 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.094182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.069382 restraints weight = 88797.887| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.67 r_work: 0.2969 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.0640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 13620 Z= 0.120 Angle : 0.586 8.871 18388 Z= 0.263 Chirality : 0.038 0.155 2120 Planarity : 0.004 0.040 2228 Dihedral : 16.901 143.620 2334 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.37 % Allowed : 13.57 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.68 (0.22), residues: 1564 helix: 2.59 (0.16), residues: 1056 sheet: -2.53 (0.48), residues: 68 loop : 0.55 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 399 TYR 0.010 0.001 TYR A 128 PHE 0.008 0.001 PHE A 242 TRP 0.006 0.001 TRP B 264 HIS 0.002 0.001 HIS D 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (13620) covalent geometry : angle 0.58579 / 0.26 (18388) hydrogen bonds : bond 0.03645 / 2.47 ( 852) hydrogen bonds : angle 4.16909 / 3.08 ( 2436) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 ILE cc_start: 0.8844 (tt) cc_final: 0.8609 (pp) outliers start: 5 outliers final: 4 residues processed: 55 average time/residue: 0.9508 time to fit residues: 59.6702 Evaluate side-chains 52 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain D residue 47 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 15 optimal weight: 1.9990 chunk 131 optimal weight: 0.0060 chunk 55 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 128 optimal weight: 0.4980 chunk 44 optimal weight: 0.0970 chunk 11 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.094567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.069815 restraints weight = 88578.725| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.67 r_work: 0.2977 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.0886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13620 Z= 0.101 Angle : 0.554 8.382 18388 Z= 0.248 Chirality : 0.037 0.159 2120 Planarity : 0.004 0.046 2228 Dihedral : 15.182 140.444 2334 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.37 % Allowed : 13.27 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.97 (0.22), residues: 1564 helix: 2.90 (0.16), residues: 1020 sheet: -2.27 (0.50), residues: 68 loop : 0.62 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 399 TYR 0.008 0.001 TYR C 245 PHE 0.007 0.001 PHE C 64 TRP 0.006 0.001 TRP B 264 HIS 0.001 0.000 HIS C 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 (13620) covalent geometry : angle 0.55396 / 0.25 (18388) hydrogen bonds : bond 0.03289 / 2.20 ( 852) hydrogen bonds : angle 3.99402 / 2.96 ( 2436) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.507 Fit side-chains revert: symmetry clash REVERT: A 55 ILE cc_start: 0.8831 (tt) cc_final: 0.8579 (pp) REVERT: A 334 MET cc_start: 0.7727 (tpp) cc_final: 0.7024 (ttp) REVERT: B 334 MET cc_start: 0.7757 (tpp) cc_final: 0.7153 (tpp) REVERT: C 334 MET cc_start: 0.7800 (tpp) cc_final: 0.7265 (tpp) REVERT: D 334 MET cc_start: 0.7721 (tpp) cc_final: 0.7189 (tpp) outliers start: 5 outliers final: 3 residues processed: 54 average time/residue: 1.0577 time to fit residues: 63.8986 Evaluate side-chains 46 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain D residue 47 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 8 optimal weight: 4.9990 chunk 143 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 144 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 117 optimal weight: 6.9990 chunk 41 optimal weight: 0.3980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.093535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.068874 restraints weight = 88837.308| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.66 r_work: 0.2959 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13620 Z= 0.118 Angle : 0.553 8.603 18388 Z= 0.249 Chirality : 0.037 0.155 2120 Planarity : 0.004 0.045 2228 Dihedral : 13.968 137.604 2332 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.59 % Allowed : 13.64 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.05 (0.22), residues: 1564 helix: 2.85 (0.16), residues: 1044 sheet: -2.25 (0.49), residues: 68 loop : 0.82 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 399 TYR 0.009 0.001 TYR A 245 PHE 0.006 0.001 PHE A 242 TRP 0.006 0.001 TRP B 264 HIS 0.001 0.000 HIS B 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (13620) covalent geometry : angle 0.55310 / 0.25 (18388) hydrogen bonds : bond 0.03321 / 2.22 ( 852) hydrogen bonds : angle 3.92004 / 2.91 ( 2436) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.516 Fit side-chains revert: symmetry clash REVERT: A 55 ILE cc_start: 0.8856 (tt) cc_final: 0.8606 (pp) REVERT: A 334 MET cc_start: 0.7704 (tpp) cc_final: 0.7204 (tpp) REVERT: B 265 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8398 (pp20) REVERT: B 334 MET cc_start: 0.7717 (tpp) cc_final: 0.7198 (tpp) REVERT: C 265 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8401 (pp20) REVERT: C 334 MET cc_start: 0.7754 (tpp) cc_final: 0.7273 (tpp) REVERT: D 334 MET cc_start: 0.7665 (tpp) cc_final: 0.7166 (tpp) outliers start: 8 outliers final: 3 residues processed: 51 average time/residue: 0.9068 time to fit residues: 51.9361 Evaluate side-chains 46 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 265 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 67 optimal weight: 5.9990 chunk 95 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 152 optimal weight: 0.9990 chunk 127 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 119 optimal weight: 0.0070 chunk 131 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.093514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.068727 restraints weight = 88241.619| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.66 r_work: 0.2962 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13620 Z= 0.106 Angle : 0.543 8.511 18388 Z= 0.243 Chirality : 0.037 0.153 2120 Planarity : 0.003 0.036 2228 Dihedral : 13.712 143.592 2330 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.29 % Allowed : 12.91 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.20 (0.22), residues: 1564 helix: 2.94 (0.16), residues: 1044 sheet: -2.05 (0.50), residues: 68 loop : 0.92 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 399 TYR 0.015 0.001 TYR A 128 PHE 0.006 0.001 PHE A 242 TRP 0.005 0.001 TRP B 264 HIS 0.001 0.000 HIS B 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (13620) covalent geometry : angle 0.54265 / 0.24 (18388) hydrogen bonds : bond 0.03196 / 2.13 ( 852) hydrogen bonds : angle 3.85676 / 2.86 ( 2436) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.721 Fit side-chains REVERT: A 55 ILE cc_start: 0.8850 (tt) cc_final: 0.8598 (pp) REVERT: A 334 MET cc_start: 0.7717 (tpp) cc_final: 0.7252 (tpp) REVERT: B 265 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8396 (pp20) REVERT: B 334 MET cc_start: 0.7728 (tpp) cc_final: 0.7221 (tpp) REVERT: C 85 LEU cc_start: 0.8952 (tp) cc_final: 0.8660 (pp) REVERT: C 334 MET cc_start: 0.7777 (tpp) cc_final: 0.7303 (tpp) REVERT: D 334 MET cc_start: 0.7730 (tpp) cc_final: 0.7226 (tpp) outliers start: 4 outliers final: 2 residues processed: 46 average time/residue: 0.9810 time to fit residues: 50.8984 Evaluate side-chains 44 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain C residue 110 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 11 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 144 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.091331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.066150 restraints weight = 88773.351| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.67 r_work: 0.2902 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13620 Z= 0.194 Angle : 0.584 8.941 18388 Z= 0.270 Chirality : 0.039 0.142 2120 Planarity : 0.004 0.036 2228 Dihedral : 14.238 141.629 2328 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.66 % Allowed : 12.98 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.08 (0.22), residues: 1564 helix: 2.81 (0.16), residues: 1044 sheet: -1.70 (0.51), residues: 68 loop : 0.91 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 311 TYR 0.012 0.001 TYR A 245 PHE 0.007 0.001 PHE C 64 TRP 0.006 0.001 TRP C 264 HIS 0.004 0.001 HIS C 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.19 (13620) covalent geometry : angle 0.58442 / 0.27 (18388) hydrogen bonds : bond 0.03680 / 2.47 ( 852) hydrogen bonds : angle 3.92399 / 2.91 ( 2436) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.624 Fit side-chains REVERT: A 26 TYR cc_start: 0.8268 (OUTLIER) cc_final: 0.7770 (m-10) REVERT: A 55 ILE cc_start: 0.8857 (tt) cc_final: 0.8595 (pp) REVERT: B 26 TYR cc_start: 0.8245 (OUTLIER) cc_final: 0.7951 (m-10) REVERT: B 265 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8422 (pp20) REVERT: C 26 TYR cc_start: 0.8252 (OUTLIER) cc_final: 0.8026 (m-10) REVERT: C 265 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8434 (pp20) REVERT: C 334 MET cc_start: 0.7731 (tpp) cc_final: 0.7193 (tpp) outliers start: 9 outliers final: 2 residues processed: 51 average time/residue: 0.9430 time to fit residues: 54.2365 Evaluate side-chains 49 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 265 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 113 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 139 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 92 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.092096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.067185 restraints weight = 88161.004| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.66 r_work: 0.2923 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13620 Z= 0.114 Angle : 0.554 8.558 18388 Z= 0.250 Chirality : 0.038 0.154 2120 Planarity : 0.003 0.035 2228 Dihedral : 13.761 144.047 2328 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.44 % Allowed : 13.13 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.22 (0.22), residues: 1564 helix: 2.91 (0.16), residues: 1044 sheet: -1.75 (0.51), residues: 68 loop : 0.98 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 81 TYR 0.013 0.001 TYR A 128 PHE 0.005 0.001 PHE A 242 TRP 0.006 0.001 TRP D 264 HIS 0.002 0.000 HIS C 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (13620) covalent geometry : angle 0.55446 / 0.25 (18388) hydrogen bonds : bond 0.03319 / 2.21 ( 852) hydrogen bonds : angle 3.84369 / 2.85 ( 2436) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.565 Fit side-chains REVERT: A 55 ILE cc_start: 0.8854 (tt) cc_final: 0.8596 (pp) REVERT: B 265 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8388 (pp20) REVERT: B 334 MET cc_start: 0.7951 (mmm) cc_final: 0.7017 (ttp) REVERT: C 265 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8387 (pp20) REVERT: C 334 MET cc_start: 0.7810 (tpp) cc_final: 0.7254 (tpp) outliers start: 6 outliers final: 2 residues processed: 48 average time/residue: 1.0550 time to fit residues: 56.8672 Evaluate side-chains 45 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 265 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 96 optimal weight: 1.9990 chunk 6 optimal weight: 0.0980 chunk 138 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 119 optimal weight: 0.5980 chunk 125 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.090993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.065919 restraints weight = 88530.864| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 2.66 r_work: 0.2897 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 13620 Z= 0.173 Angle : 0.578 8.769 18388 Z= 0.265 Chirality : 0.038 0.148 2120 Planarity : 0.004 0.035 2228 Dihedral : 13.944 142.121 2328 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.88 % Allowed : 12.68 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.16 (0.22), residues: 1564 helix: 2.83 (0.16), residues: 1044 sheet: -1.54 (0.52), residues: 68 loop : 1.02 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 311 TYR 0.015 0.001 TYR B 128 PHE 0.006 0.001 PHE C 64 TRP 0.007 0.001 TRP A 264 HIS 0.003 0.001 HIS B 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 (13620) covalent geometry : angle 0.57846 / 0.26 (18388) hydrogen bonds : bond 0.03564 / 2.39 ( 852) hydrogen bonds : angle 3.87209 / 2.87 ( 2436) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 time to evaluate : 0.588 Fit side-chains REVERT: A 55 ILE cc_start: 0.8852 (tt) cc_final: 0.8588 (pp) REVERT: B 26 TYR cc_start: 0.8208 (OUTLIER) cc_final: 0.7899 (m-10) REVERT: B 265 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8412 (pp20) REVERT: C 265 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8413 (pp20) REVERT: D 26 TYR cc_start: 0.8226 (OUTLIER) cc_final: 0.7591 (m-80) outliers start: 12 outliers final: 2 residues processed: 54 average time/residue: 0.8757 time to fit residues: 54.2502 Evaluate side-chains 48 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 265 GLU Chi-restraints excluded: chain D residue 26 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 85 optimal weight: 0.8980 chunk 51 optimal weight: 0.4980 chunk 55 optimal weight: 0.9980 chunk 149 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 138 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.091789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.066760 restraints weight = 88747.545| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.68 r_work: 0.2918 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13620 Z= 0.118 Angle : 0.560 8.554 18388 Z= 0.252 Chirality : 0.038 0.155 2120 Planarity : 0.003 0.034 2228 Dihedral : 13.579 144.337 2328 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.22 % Allowed : 12.91 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.27 (0.22), residues: 1564 helix: 2.92 (0.16), residues: 1044 sheet: -1.59 (0.51), residues: 68 loop : 1.05 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 81 TYR 0.009 0.001 TYR A 170 PHE 0.005 0.001 PHE A 242 TRP 0.006 0.001 TRP C 264 HIS 0.002 0.000 HIS C 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (13620) covalent geometry : angle 0.55999 / 0.25 (18388) hydrogen bonds : bond 0.03302 / 2.20 ( 852) hydrogen bonds : angle 3.80382 / 2.82 ( 2436) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 42 time to evaluate : 0.670 Fit side-chains REVERT: A 55 ILE cc_start: 0.8849 (tt) cc_final: 0.8588 (pp) REVERT: C 334 MET cc_start: 0.7955 (mmm) cc_final: 0.6924 (ttp) outliers start: 3 outliers final: 1 residues processed: 45 average time/residue: 1.0765 time to fit residues: 54.4247 Evaluate side-chains 42 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 41 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 127 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.091630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.066705 restraints weight = 88618.597| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.67 r_work: 0.2915 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13620 Z= 0.130 Angle : 0.563 8.621 18388 Z= 0.254 Chirality : 0.038 0.150 2120 Planarity : 0.004 0.034 2228 Dihedral : 13.444 143.568 2328 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.29 % Allowed : 12.83 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.25 (0.22), residues: 1564 helix: 2.92 (0.16), residues: 1048 sheet: -1.53 (0.52), residues: 68 loop : 0.98 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 81 TYR 0.015 0.001 TYR A 128 PHE 0.005 0.001 PHE D 242 TRP 0.007 0.001 TRP C 264 HIS 0.002 0.001 HIS C 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (13620) covalent geometry : angle 0.56280 / 0.25 (18388) hydrogen bonds : bond 0.03319 / 2.21 ( 852) hydrogen bonds : angle 3.78443 / 2.81 ( 2436) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.581 Fit side-chains REVERT: A 55 ILE cc_start: 0.8857 (tt) cc_final: 0.8596 (pp) outliers start: 4 outliers final: 1 residues processed: 44 average time/residue: 0.9085 time to fit residues: 45.5002 Evaluate side-chains 41 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 40 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 42 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 38 optimal weight: 0.1980 chunk 123 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.091925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.067106 restraints weight = 87753.532| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.66 r_work: 0.2929 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13620 Z= 0.109 Angle : 0.558 8.946 18388 Z= 0.249 Chirality : 0.037 0.154 2120 Planarity : 0.003 0.034 2228 Dihedral : 13.126 144.314 2328 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.29 % Allowed : 12.83 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.32 (0.22), residues: 1564 helix: 2.97 (0.16), residues: 1048 sheet: -1.55 (0.52), residues: 68 loop : 1.01 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 399 TYR 0.008 0.001 TYR D 128 PHE 0.005 0.001 PHE D 242 TRP 0.006 0.001 TRP D 264 HIS 0.002 0.000 HIS C 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (13620) covalent geometry : angle 0.55758 / 0.25 (18388) hydrogen bonds : bond 0.03191 / 2.12 ( 852) hydrogen bonds : angle 3.73392 / 2.77 ( 2436) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7698.56 seconds wall clock time: 130 minutes 40.70 seconds (7840.70 seconds total)